The Technology Partnership / Mbed OS LEX_Threaded_Programming_V3

LEX_Threaded_Programming

Dependencies:   Heater_V2 MODSERIAL Nanopb FastPWM ADS8568_ADC

main.cpp@9:9474da78cec3, 2019-09-12 (annotated)

Committer:
justinbuckland
Date:
Thu Sep 12 12:43:07 2019 +0000
Revision:
9:9474da78cec3
Parent:
8:58c6d51957df
Child:
10:f8202e71e765
Update to trigger camera

Who changed what in which revision?

UserRevisionLine numberNew contents of line
omatthews 0:54bedd3964e2 1 #include "mbed.h"
omatthews 0:54bedd3964e2 2 #include "pb.h"
omatthews 0:54bedd3964e2 3 #include "pb_decode.h"
omatthews 0:54bedd3964e2 4 #include "pb_encode.h"
omatthews 0:54bedd3964e2 5 #include "MODSERIAL.h"
omatthews 0:54bedd3964e2 6 #include "ADS8568_ADC.h"
omatthews 0:54bedd3964e2 7 #include "Heater.h"
omatthews 0:54bedd3964e2 8 #include "FastPWM.h"
omatthews 0:54bedd3964e2 9 #include "memspcr.pb.h"
omatthews 0:54bedd3964e2 10 #include <vector>
omatthews 0:54bedd3964e2 11 #include <iterator>
omatthews 0:54bedd3964e2 12
justinbuckland 8:58c6d51957df 13 #define BUFFER_SIZE 4096
justinbuckland 9:9474da78cec3 14 #define LED_PULSE_PERIOD 8400 // ticks, 10kHz when CPU clock is 84MHz
justinbuckland 9:9474da78cec3 15 #define LED_PULSE_WIDTH 4200 // ticks, 50% duty cycle
justinbuckland 8:58c6d51957df 16
omatthews 0:54bedd3964e2 17 Heater * heater;
intrinseca 4:63d7f2a0dec6 18 float r_gradient; //setpoint setting
omatthews 5:702b32ead94e 19
omatthews 0:54bedd3964e2 20
justinbuckland 8:58c6d51957df 21 MODSERIAL pc(PA_9, PA_10, BUFFER_SIZE); //mcu TX, RX, BUFFER_SIZE byte TX and RX buffers
omatthews 0:54bedd3964e2 22 ADS8568_ADC adc(PB_15, PB_14, PB_13, PB_12, PC_15, PC_0, PC_1, PC_2, PC_3);
omatthews 0:54bedd3964e2 23 I2C i2c(PB_7, PB_8); //SDA, SCL
omatthews 0:54bedd3964e2 24 Timer timer;
omatthews 0:54bedd3964e2 25 DigitalIn adc_busy(PA_8); //Busy interrupt sig#
omatthews 5:702b32ead94e 26
omatthews 0:54bedd3964e2 27
omatthews 0:54bedd3964e2 28 //Heater Control
omatthews 5:702b32ead94e 29 FastPWM drive_main(PC_9);
omatthews 5:702b32ead94e 30 FastPWM drive_lysis(PC_8);
omatthews 5:702b32ead94e 31 FastPWM guard_main(PC_7);
omatthews 5:702b32ead94e 32 FastPWM guard_lysis(PC_6);
justinbuckland 7:a4fc853feb30 33
justinbuckland 7:a4fc853feb30 34 int heater_ID_main = 1;
justinbuckland 7:a4fc853feb30 35 int heater_ID_lysis = 2;
omatthews 5:702b32ead94e 36 int i_port_main = 0;
omatthews 5:702b32ead94e 37 int i_port_lysis = 2;
omatthews 5:702b32ead94e 38 int v_port_main = 1;
omatthews 5:702b32ead94e 39 int v_port_lysis = 3;
omatthews 0:54bedd3964e2 40
justinbuckland 7:a4fc853feb30 41 int heater_ID = 0;
omatthews 0:54bedd3964e2 42
justinbuckland 9:9474da78cec3 43 //Illumination LED Control
justinbuckland 9:9474da78cec3 44
omatthews 0:54bedd3964e2 45
justinbuckland 7:a4fc853feb30 46 //Indicator LEDs
omatthews 0:54bedd3964e2 47 DigitalOut hb_led(PC_13); //Green
omatthews 0:54bedd3964e2 48 DigitalOut led_0(PC_4); //Red
omatthews 0:54bedd3964e2 49 DigitalOut led_1(PC_5); //Green
omatthews 0:54bedd3964e2 50
justinbuckland 7:a4fc853feb30 51 //Camera and LED drive
justinbuckland 7:a4fc853feb30 52 DigitalOut camTrigger(PB_2); //Trigger camera
justinbuckland 9:9474da78cec3 53 FastPWM ledDrive(PB_4); //PWM drive LED for fluorescence detection
justinbuckland 7:a4fc853feb30 54
omatthews 0:54bedd3964e2 55 //User buttons
omatthews 0:54bedd3964e2 56 DigitalIn user_0(PB_0);
omatthews 0:54bedd3964e2 57 DigitalIn user_1(PB_1);
omatthews 0:54bedd3964e2 58
omatthews 0:54bedd3964e2 59 BusOut converts(PC_0, PC_1, PC_2, PC_3);
omatthews 0:54bedd3964e2 60
omatthews 0:54bedd3964e2 61 //Threads
omatthews 6:ef2bcc5fe3af 62 Thread heater_control(osPriorityHigh);
omatthews 6:ef2bcc5fe3af 63 Thread logging_thread(osPriorityAboveNormal);
omatthews 0:54bedd3964e2 64
omatthews 0:54bedd3964e2 65 //Tickers
omatthews 0:54bedd3964e2 66 Ticker heat_tick;
omatthews 0:54bedd3964e2 67 Ticker pressure_tick;
omatthews 0:54bedd3964e2 68 Ticker log_tick;
omatthews 0:54bedd3964e2 69
omatthews 0:54bedd3964e2 70
omatthews 0:54bedd3964e2 71 //Flags
omatthews 5:702b32ead94e 72 EventFlags flags; //Flags:
omatthews 5:702b32ead94e 73 // 0 => update heater
omatthews 5:702b32ead94e 74 // 1 => log state
omatthews 5:702b32ead94e 75 bool triggered_flag;
omatthews 0:54bedd3964e2 76 bool status = true;
omatthews 0:54bedd3964e2 77
omatthews 0:54bedd3964e2 78 //Configuration data
omatthews 0:54bedd3964e2 79 memspcr_ExperimentConfiguration exp_config = memspcr_ExperimentConfiguration_init_zero;
omatthews 0:54bedd3964e2 80 int buffer_length;
omatthews 0:54bedd3964e2 81 size_t message_length;
justinbuckland 8:58c6d51957df 82 uint8_t buffer[BUFFER_SIZE];
omatthews 0:54bedd3964e2 83
omatthews 0:54bedd3964e2 84
omatthews 0:54bedd3964e2 85 //Functions for reading and decoding the message__________________________________________________
omatthews 0:54bedd3964e2 86
omatthews 0:54bedd3964e2 87 void read_message()
omatthews 0:54bedd3964e2 88 {
justinbuckland 7:a4fc853feb30 89 if (pc.scanf("%d",&message_length) < 0){pc.printf("# Error reading message length");}
omatthews 5:702b32ead94e 90 size_t buffer_length = sizeof(buffer);
omatthews 5:702b32ead94e 91 if (message_length > buffer_length)
omatthews 5:702b32ead94e 92 {
justinbuckland 7:a4fc853feb30 93 pc.printf("# Message length exceeds buffer. \n Input configuration file\n");
omatthews 5:702b32ead94e 94 read_message();
omatthews 5:702b32ead94e 95 return;
omatthews 5:702b32ead94e 96 }
justinbuckland 7:a4fc853feb30 97 pc.printf("# Message is %d chars long, buffer length is %d\n",message_length,buffer_length);
omatthews 5:702b32ead94e 98 unsigned int c;
omatthews 5:702b32ead94e 99 for (int i = 0; i < message_length; i++)
omatthews 0:54bedd3964e2 100 {
omatthews 0:54bedd3964e2 101 pc.scanf("%02X",&c);
omatthews 0:54bedd3964e2 102 buffer[i] = (char) c;
omatthews 0:54bedd3964e2 103 }
omatthews 0:54bedd3964e2 104 }
omatthews 0:54bedd3964e2 105
omatthews 0:54bedd3964e2 106 void decode_message()
omatthews 0:54bedd3964e2 107 {
omatthews 5:702b32ead94e 108 // Create a stream that reads from the buffer.
omatthews 5:702b32ead94e 109
omatthews 0:54bedd3964e2 110 pb_istream_t istream = pb_istream_from_buffer(buffer, message_length);
omatthews 0:54bedd3964e2 111
omatthews 5:702b32ead94e 112 //Now we are ready to decode the message.
omatthews 0:54bedd3964e2 113 status = pb_decode(&istream, memspcr_ExperimentConfiguration_fields, &exp_config);
omatthews 0:54bedd3964e2 114
omatthews 5:702b32ead94e 115 // Check for errors...
omatthews 5:702b32ead94e 116 if (!status) {
justinbuckland 7:a4fc853feb30 117 pc.printf("# Decoding failed: %s\n", PB_GET_ERROR(&istream));
omatthews 0:54bedd3964e2 118 }
omatthews 0:54bedd3964e2 119 }
omatthews 0:54bedd3964e2 120
omatthews 0:54bedd3964e2 121 bool decode_callback(pb_istream_t *stream, const pb_field_t *field, void **arg)
omatthews 0:54bedd3964e2 122 {
omatthews 0:54bedd3964e2 123 vector <memspcr_ThermalStep> * dest = (vector <memspcr_ThermalStep> *)(*arg);
omatthews 0:54bedd3964e2 124 memspcr_ThermalStep result = memspcr_ThermalStep_init_zero;
omatthews 0:54bedd3964e2 125 status = pb_decode(stream, memspcr_ThermalStep_fields, & result);
omatthews 5:702b32ead94e 126
omatthews 5:702b32ead94e 127 if (!status) {
justinbuckland 7:a4fc853feb30 128 pc.printf("# Decode callback failed\n");
omatthews 0:54bedd3964e2 129 }
omatthews 0:54bedd3964e2 130
intrinseca 4:63d7f2a0dec6 131 dest->push_back(result); //CHECK: Does result get copied into the vector?
omatthews 0:54bedd3964e2 132 return true;
omatthews 0:54bedd3964e2 133 }
omatthews 0:54bedd3964e2 134
omatthews 0:54bedd3964e2 135
omatthews 0:54bedd3964e2 136 //Ticking functions_________________________________________________________________
omatthews 0:54bedd3964e2 137
omatthews 6:ef2bcc5fe3af 138
omatthews 5:702b32ead94e 139 void temp_trigger()
omatthews 0:54bedd3964e2 140 {
omatthews 5:702b32ead94e 141 //This function triggers a temperature update.
omatthews 5:702b32ead94e 142 //N.B. update cannot be called directly from a ticker as tickers and
omatthews 0:54bedd3964e2 143 //reading the ADC both rely on interrupts.
omatthews 5:702b32ead94e 144 flags.set(0x1);
omatthews 0:54bedd3964e2 145 }
omatthews 0:54bedd3964e2 146
omatthews 6:ef2bcc5fe3af 147
omatthews 6:ef2bcc5fe3af 148
omatthews 2:b27d8f9a6e49 149 void log_trigger()
omatthews 2:b27d8f9a6e49 150 {
omatthews 5:702b32ead94e 151 flags.set(0x2);
omatthews 2:b27d8f9a6e49 152 }
justinbuckland 7:a4fc853feb30 153
omatthews 5:702b32ead94e 154 void pressure_control()
omatthews 0:54bedd3964e2 155 {
omatthews 0:54bedd3964e2 156 //Input pressure control function here
omatthews 0:54bedd3964e2 157 //i.e.
omatthews 0:54bedd3964e2 158 //read_pressure();
omatthews 0:54bedd3964e2 159 //if (pressure < lower_bound) {
omatthews 5:702b32ead94e 160 //pump_turn_on();
omatthews 5:702b32ead94e 161 //}
omatthews 0:54bedd3964e2 162 //else if (pressure > upper_bound) {
omatthews 5:702b32ead94e 163 //pump_turn_off();
omatthews 5:702b32ead94e 164 //}
omatthews 0:54bedd3964e2 165 led_1 = !led_1;
omatthews 0:54bedd3964e2 166 }
omatthews 0:54bedd3964e2 167
omatthews 2:b27d8f9a6e49 168
omatthews 0:54bedd3964e2 169
omatthews 0:54bedd3964e2 170
omatthews 5:702b32ead94e 171 //Other functions__________________________________________________________________
omatthews 0:54bedd3964e2 172
omatthews 0:54bedd3964e2 173
omatthews 0:54bedd3964e2 174 void temp_control() {
omatthews 0:54bedd3964e2 175 while(1){
omatthews 6:ef2bcc5fe3af 176 flags.wait_any(0x1,osWaitForever,true);
omatthews 0:54bedd3964e2 177 heater->read();
omatthews 0:54bedd3964e2 178 heater->update();
omatthews 0:54bedd3964e2 179 }
omatthews 0:54bedd3964e2 180 }
omatthews 5:702b32ead94e 181
omatthews 2:b27d8f9a6e49 182 void log_state()
omatthews 2:b27d8f9a6e49 183 {
omatthews 2:b27d8f9a6e49 184 while(1){
omatthews 6:ef2bcc5fe3af 185 flags.wait_any(0x2,osWaitForever,true);
omatthews 6:ef2bcc5fe3af 186 //Output time, R_ref, R, error, error_integrated
justinbuckland 7:a4fc853feb30 187 pc.printf("%10d,%10d,%10.6f,%10.6f\n", heater_ID, timer.read_ms(), heater->Get_R(), heater->Get_R_ref());
omatthews 2:b27d8f9a6e49 188 }
omatthews 2:b27d8f9a6e49 189 }
omatthews 5:702b32ead94e 190
omatthews 5:702b32ead94e 191 void set_point_routine(std::vector<memspcr_ThermalStep> profile) {
omatthews 5:702b32ead94e 192 int curr_time;
omatthews 5:702b32ead94e 193 vector <memspcr_ThermalStep>::iterator it_prev, it = profile.begin();
omatthews 5:702b32ead94e 194 if (it->elapsed_time_ms != 0)
omatthews 5:702b32ead94e 195 {
justinbuckland 7:a4fc853feb30 196 pc.printf("# Error: the first point in the profile should be at time 0.\n");
omatthews 5:702b32ead94e 197 return;
omatthews 5:702b32ead94e 198 }
omatthews 2:b27d8f9a6e49 199 it++;
omatthews 0:54bedd3964e2 200
omatthews 0:54bedd3964e2 201 for (it_prev = profile.begin(); it < profile.end(); it ++, it_prev++){
omatthews 0:54bedd3964e2 202 triggered_flag = false;
omatthews 0:54bedd3964e2 203 r_gradient = (it->resistance - it_prev->resistance)/(it->elapsed_time_ms - it_prev->elapsed_time_ms);
omatthews 0:54bedd3964e2 204 while ((curr_time = timer.read_ms()) <= it->elapsed_time_ms){
omatthews 5:702b32ead94e 205 heater->Set_ref(it_prev->resistance + r_gradient * (curr_time - it_prev->elapsed_time_ms));
justinbuckland 8:58c6d51957df 206
justinbuckland 9:9474da78cec3 207 if (!triggered_flag && (it->camera_offset_ms != 0) && (curr_time > it_prev->elapsed_time_ms + it->camera_offset_ms))
omatthews 0:54bedd3964e2 208 {
justinbuckland 9:9474da78cec3 209 //Start camera exposure and turn on LED if camera_offset_ms is non-zero
justinbuckland 7:a4fc853feb30 210 camTrigger = 0;
justinbuckland 7:a4fc853feb30 211 wait_us(10);
justinbuckland 7:a4fc853feb30 212 camTrigger = 1;
justinbuckland 7:a4fc853feb30 213 led_0 = 1;
justinbuckland 9:9474da78cec3 214 ledDrive.pulsewidth_ticks(LED_PULSE_WIDTH);
omatthews 0:54bedd3964e2 215 triggered_flag = true;
omatthews 0:54bedd3964e2 216 }
justinbuckland 8:58c6d51957df 217 wait_us(200);
omatthews 0:54bedd3964e2 218 }
justinbuckland 8:58c6d51957df 219 //Stop camera exposure and turn off LED at end of time segment
justinbuckland 8:58c6d51957df 220 camTrigger = 0;
justinbuckland 9:9474da78cec3 221 ledDrive.pulsewidth_ticks(0);
justinbuckland 8:58c6d51957df 222 led_0 = 0;
omatthews 0:54bedd3964e2 223 }
omatthews 0:54bedd3964e2 224 }
omatthews 0:54bedd3964e2 225
omatthews 0:54bedd3964e2 226
omatthews 5:702b32ead94e 227 int main()
omatthews 5:702b32ead94e 228 {
omatthews 0:54bedd3964e2 229 pc.baud(115200);
omatthews 0:54bedd3964e2 230 adc.init();
omatthews 5:702b32ead94e 231
omatthews 0:54bedd3964e2 232 buffer_length = sizeof(buffer)/sizeof(uint8_t);
justinbuckland 7:a4fc853feb30 233 pc.printf("# Input configuration file\n");
omatthews 5:702b32ead94e 234
justinbuckland 9:9474da78cec3 235 //set up LED PWM drive
justinbuckland 9:9474da78cec3 236 ledDrive.prescaler(1);
justinbuckland 9:9474da78cec3 237 ledDrive.period_ticks(LED_PULSE_PERIOD);
justinbuckland 9:9474da78cec3 238 ledDrive.pulsewidth_ticks(0);
justinbuckland 9:9474da78cec3 239
intrinseca 4:63d7f2a0dec6 240 //set up nanopb
omatthews 5:702b32ead94e 241 std::vector<memspcr_ThermalStep> profile;
omatthews 5:702b32ead94e 242 exp_config.profile.funcs.decode = decode_callback;
omatthews 5:702b32ead94e 243 exp_config.profile.arg = &profile;
omatthews 5:702b32ead94e 244
intrinseca 4:63d7f2a0dec6 245 //read and decode configuration
intrinseca 4:63d7f2a0dec6 246 read_message();
justinbuckland 7:a4fc853feb30 247 pc.printf("# Message read\n");
omatthews 0:54bedd3964e2 248 decode_message();
justinbuckland 7:a4fc853feb30 249 pc.printf("# Message decoded\n");
omatthews 5:702b32ead94e 250
omatthews 6:ef2bcc5fe3af 251 Heater * heater_main = new Heater(i_port_main, v_port_main, & drive_main, & guard_main, & adc, adc_busy, exp_config.thermal);
omatthews 6:ef2bcc5fe3af 252 Heater * heater_lysis = new Heater(i_port_lysis, v_port_lysis, & drive_lysis, & guard_lysis, & adc, adc_busy, exp_config.thermal);
omatthews 5:702b32ead94e 253
omatthews 5:702b32ead94e 254 //Select heater. Put control times in us for ticker functions
omatthews 5:702b32ead94e 255 if (exp_config.selected_heater == memspcr_ExperimentConfiguration_Heater_MAIN) {
omatthews 5:702b32ead94e 256 heater = heater_main;
justinbuckland 7:a4fc853feb30 257 heater_ID = heater_ID_main;
omatthews 5:702b32ead94e 258 } else if (exp_config.selected_heater == memspcr_ExperimentConfiguration_Heater_LYSIS) {
omatthews 5:702b32ead94e 259 heater = heater_lysis;
justinbuckland 7:a4fc853feb30 260 heater_ID = heater_ID_lysis;
omatthews 5:702b32ead94e 261 } else {
justinbuckland 8:58c6d51957df 262 pc.printf("# Error - no heater has been selected\n");
omatthews 5:702b32ead94e 263 return 1;
omatthews 5:702b32ead94e 264 }
omatthews 5:702b32ead94e 265
justinbuckland 7:a4fc853feb30 266 pc.printf("# Starting pressure control\n");
omatthews 0:54bedd3964e2 267 pressure_tick.attach(& pressure_control, 1);
justinbuckland 7:a4fc853feb30 268 pc.printf("# Waiting for start signal to begin temperature control (type in an s or press button 0)\n");
omatthews 6:ef2bcc5fe3af 269 heater->Set_ref(0.0);
omatthews 6:ef2bcc5fe3af 270 heater_control.start(& temp_control);
omatthews 6:ef2bcc5fe3af 271 heat_tick.attach_us(& temp_trigger,exp_config.thermal.control_loop_interval_ms * 1000);
omatthews 6:ef2bcc5fe3af 272
omatthews 2:b27d8f9a6e49 273 while (pc.getcNb()!='s' && !user_0);
omatthews 5:702b32ead94e 274
justinbuckland 8:58c6d51957df 275 pc.printf("# Start signal received\n");
omatthews 0:54bedd3964e2 276
omatthews 2:b27d8f9a6e49 277 logging_thread.start(& log_state);
omatthews 6:ef2bcc5fe3af 278 log_tick.attach_us(& log_trigger,exp_config.logging_interval_ms * 1000);
omatthews 0:54bedd3964e2 279
justinbuckland 7:a4fc853feb30 280 pc.printf("# Starting routine\n");
justinbuckland 7:a4fc853feb30 281 pc.printf("# heater, time(ms), r, rSet\n");
omatthews 2:b27d8f9a6e49 282 timer.start();
omatthews 5:702b32ead94e 283 set_point_routine(profile);
omatthews 6:ef2bcc5fe3af 284
omatthews 6:ef2bcc5fe3af 285 //Turn off
omatthews 5:702b32ead94e 286 heat_tick.detach();
omatthews 5:702b32ead94e 287 log_tick.detach();
omatthews 5:702b32ead94e 288 wait(1);
omatthews 2:b27d8f9a6e49 289 heater->turn_off();
justinbuckland 8:58c6d51957df 290
justinbuckland 8:58c6d51957df 291
justinbuckland 7:a4fc853feb30 292 pc.printf("# Finished\n");
justinbuckland 7:a4fc853feb30 293
omatthews 5:702b32ead94e 294 return 0;
omatthews 5:702b32ead94e 295 }